Reading your original post it appears you want to install a 2nd or 3rd (motor home)12volt system independent of the existing system(s)
(On a motor home one system is the "Truck Parts" (Motor) and the 2nd (Which is common to trailers)is "Home".
So long as the system is independent...There can not POSSIBLY be a problem. (Assumes proper installation methods were used)
IF you want to parallel this new 12 volt system with the existing one... That too should work.
NOTE: you are not installing two Six volt batteries so much as a single BIG 12volt battery in 2 pieces....Think of the pair that way, As a single 12volt,Many questions go POOF if you do that.
DO pay attention to Polarity. AND use proper fuses